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DOE OSTI2021

Probing photosynthesis by altering chloroplast proteins (Final Technical Report)

The goal of this project was to explore the effect of altering the carbon fixing enzyme Rubisco in the model C3 plant tobacco on photosynthesis and plant growth and development. We introduced the gene sequences encoding Rubisco from a Limonium species and from a red alga into tobacco and found that the enzyme did not assemble properly, undoubtedly requiring additional assembly factors from the source organism. We then developed a method to make single amino-acid changes into the Rubisco subunit that is encoded by the chloroplast genome. We used the method to investigate the role of particular amino acid residues in kinetic properties of Rubisco. Finally, we improved a bacterial expression system that has allowed assembly of active tobacco Rubisco in E. coli. We used the improved system to investigate the kinetic properties of Rubisco enzymes that contain only one type of Rubisco small subunit along with the large subunit.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Unconventional genetic code systems in archaea

Archaea constitute the third domain of life, distinct from bacteria and eukaryotes given their ability to tolerate extreme environments. To survive these harsh conditions, certain archaeal lineages possess unique genetic code systems to encode either selenocysteine or pyrrolysine, rare amino acids not found in all organisms. Furthermore, archaea utilize alternate tRNA-dependent pathways to biosynthesize and incorporate members of the 20 canonical amino acids. Recent discoveries of new archaeal species have revealed the co-occurrence of these genetic code systems within a single lineage. This review discusses the diverse genetic code systems of archaea, while detailing the associated biochemical elements and molecular mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1999

Oligomerization of L-gamma-carboxyglutamic acid

Unlike glutamic acid, L-gamma-carboxyglutamic acid does not oligomerize efficiently when treated with carbonyldiimidazole in aqueous solution. However, divalent ions such as Mg2+ catalyze the reaction, and lead to the formation of oligomers in good yield. In the presence of hydroxylapatite, L-gamma-carboxyglutamic acid oligomerizes efficiently in a reaction that proceeds in the absence of divalent ions but is further catalyzed when they are present. After 'feeding' 50 times with activated amino acid in the presence of the Mg2+ ion, oligomers longer than the 20-mer could be detected. The effect of hydroxylapatite on peptide elongation is very sensitive to the nature of the activated amino acid and the acceptor peptide. Glutamic acid oligomerizes more efficiently than L-gamma-carboxyglutamic acid on hydroxylapatite and adds more efficiently to decaglutamic acid in solution. One might, therefore, expect that glutamic acid would add more efficiently than L-gamma-carboxyglutamic acid to decaglutamic acid on hydroxylapatite. The contrary is true--the addition of L-gamma-carboxyglutamic acid is substantially more efficient. This suggests that oligomerization on the surface of hydroxylapatite depends on the detailed match between the structure of the surface of the mineral and the structure of the oligomer.

Non-NASA Center↗

DOE OSTI2014

A mutant (‘lab strain’) of the hyperthermophilic archaeon Pyrococcus furiosus , lacking flagella, has unusual growth physiology

In this paper, a mutant (‘lab strain’) of the hyperthermophilic archaeon Pyrococcus furiosus DSM3638 exhibited an extended exponential phase and atypical cell aggregation behavior. Genomic DNA from the mutant culture was sequenced and compared to wild-type (WT) DSM3638, revealing 145 genes with one or more insertions, deletions, or substitutions (12 silent, 33 amino acid substitutions, and 100 frame shifts). Approximately, half of the mutated genes were transposases or hypothetical proteins. The WT transcriptome revealed numerous changes in amino acid and pyrimidine biosynthesis pathways coincidental with growth phase transitions, unlike the mutant whose transcriptome reflected the observed prolonged exponential phase. Targeted gene deletions, based on frame-shifted ORFs in the mutant genome, in a genetically tractable strain of P. furiosus (COM1) could not generate the extended exponential phase behavior observed for the mutant. For example, a putative radical SAM family protein (PF2064) was the most highly up-regulated ORF (>25-fold) in the WT between exponential and stationary phase, although this ORF was unresponsive in the mutant; deletion of this gene in P. furiosus COM1 resulted in no apparent phenotype. On the other hand, frame-shifting mutations in the mutant genome negatively impacted transcription of a flagellar biosynthesis operon (PF0329-PF0338).Consequently, cells in the mutant culture lacked flagella and, unlike the WT, showed minimal evidence of exopolysaccharide-based cell aggregation in post-exponential phase. Finally, electron microscopy of PF0331-PF0337 deletions in P. furiosus COM1 showed that absence of flagella impacted normal cell aggregation behavior and, furthermore, indicated that flagella play a key role, beyond motility, in the growth physiology of P. furiosus.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

Understanding the Heating Kinetics of Asteroid Ryugu By Comparison to Naturally and Experimentally Heated Meteorites

The Hayabusa2 mission visited the near-Earth Cb-type asteroid (162173) Ryugu and has returned to Earth surface material of Ryugu. Ryugu is an airless rubble pile asteroid exposed to space weathering [1]. Visible and near infrared remote observations recorded an absorption feature at 2.72 μm indicating the presence of OH– bearing hydrous components. The weak 2.72 μm feature suggested that Ryugu was once organic- and water-rich and subsequently dehydrated by a brief period of surficial heating with resemblance to “thermally metamorphosed carbonaceous chondrites”, “CI-/CM-like”, or “CY” chondrites [2, 3]. However, initial examination of the returned samples did not identify any significant heating of >150 °C [4, 5], and contrastingly, amino acid analysis of Ryugu samples suggested similarities to thermally-altered meteorites on the grounds of the predominant straight-chain n-ω-amino acid abundances [6]. In this study, we aim at addressing the nonconformal interpretations to the thermal history of Ryugu by comparing the organic composition of fresh Ryugu samples to that of chondritic meteorites that have been naturally (long-term radiogenic thermal metamorphism and short-term heating) and experimentally heated.

Q. H. S. Chan↗

DOE OSTI2012

Acid Stability of the Hemagglutinin Protein Regulates H5N1 Influenza Virus Pathogenicity

Highly pathogenic avian influenza viruses of the H5N1 subtype continue to threaten agriculture and human health. Here, we use biochemistry and x-ray crystallography to reveal how amino-acid variations in the hemagglutinin (HA) protein contribute to the pathogenicity of H5N1 influenza virus in chickens. HA proteins from highly pathogenic (HP) A/chicken/Hong Kong/YU562/2001 and moderately pathogenic (MP) A/goose/Hong Kong/437-10/1999 isolates of H5N1 were found to be expressed and cleaved in similar amounts, and both proteins had similar receptor-binding properties. However, amino-acid variations at positions 104 and 115 in the vestigial esterase sub-domain of the HA1 receptor-binding domain (RBD) were found to modulate the pH of HA activation such that the HP and MP HA proteins are activated for membrane fusion at pH 5.7 and 5.3, respectively. In general, an increase in H5N1 pathogenicity in chickens was found to correlate with an increase in the pH of HA activation for mutant and chimeric HA proteins in the observed range of pH 5.2 to 6.0. We determined a crystal structure of the MP HA protein at 2.50 {angstrom} resolution and two structures of HP HA at 2.95 and 3.10 {angstrom} resolution. Residues 104 and 115 that modulate the acid stability of the HA protein are situated at the N- and C-termini of the 110-helix in the vestigial esterase sub-domain, which interacts with the B loop of the HA2 stalk domain. Interactions between the 110-helix and the stalk domain appear to be important in regulating HA protein acid stability, which in turn modulates influenza virus replication and pathogenesis. Overall, an optimal activation pH of the HA protein is found to be necessary for high pathogenicity by H5N1 influenza virus in avian species.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

RrA, an enzyme from Rhodospirillum rubrum , is a prototype of a new family of short‐chain L‐asparaginases

Abstract L‐Asparaginases (ASNases) catalyze the hydrolysis of L‐Asn to L‐Asp and ammonia. Members of the ASNase family are used as drugs in the treatment of leukemia, as well as in the food industry. The protomers of bacterial ASNases typically contain 300–400 amino acids (typical class 1 ASNases). In contrast, the chain of ASNase from Rhodospirillum rubrum , reported here and referred to as RrA, consists of only 172 amino acid residues. RrA is homologous to the N‐terminal domain of typical bacterial class 1 ASNases and exhibits millimolar affinity for L‐Asn. In this study, we demonstrate that RrA belongs to a unique family of cytoplasmic, short‐chain ASNases (scASNases). These proteins occupy a distinct region in the sequence space, separate from the regions typically assigned to class 1 ASNases. The scASNases are present in approximately 7% of eubacterial species, spanning diverse bacterial lineages. They seem to be significantly enriched in species that encode for more than one class 1 ASNase. Here, we report biochemical, biophysical, and structural properties of RrA, a member of scASNases family. Crystal structures of the wild‐type RrA, both with and without bound L‐Asp, as well as structures of several RrA mutants, reveal topologically unique tetramers. Moreover, the active site of one protomer is complemented by two residues (Tyr21 and Asn26) from another protomer. Upon closer inspection, these findings clearly outline scASNases as a stand‐alone subfamily of ASNases that can catalyze the hydrolysis of L‐Asn to L‐Asp despite the lack of the C‐terminal domain that is present in all ASNases described structurally to date.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Effect of histidine on sorafenib-induced vascular damage: Analysis using novel medaka fish model

Highlights: • Sorafenib decreased blood flow in the vasculature by narrowing the vascular diameter. • Histidine maintained the blood flow by dilating the vascular diameter of the existing vessel. • Histidine was useful for managing the sorafenib related vascular damage. • No positive effect of histidine was seen on the tumor progression or on the novel regenerating vessels. • A fli::GFP transgenic medaka is useful for analyzing the vascular changes under the administration of these chemicals. Sorafenib (SFN) is an anti-angiogenic chemotherapeutic that prolongs survival of patients with hepatocellular carcinoma (HCC); its side effects, including vascular damages such as hand-foot syndrome (HFS), are a major cause of therapy discontinuation. We previously reported that maintenance of peripheral blood flow by intake of dried bonito broth (DBB) significantly prevented HFS and prolonged the administration period. The amino acids contained in DBB probably contribute to its effects, but the mechanism has not been clarified. We hypothesized that histidine, the largest component among the amino acids contained in DBB, has effects on SFN-induced vascular damage, and evaluated this possibility using a novel medaka fish model.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Chloroplast stromal processing peptidase activity is modulated by transit peptide determinants that include inhibitory roles for its N-terminal domain and initial Met

Highlights: • Inactivation of SPP is not through a “cysteine switch” mechanism. • Thiol-modifying reagents do not stimulate preSPP activity but diminish mature SPP activity. • NEM disrupts both substrate binding and peptide bond cleavage by SPP. • Deletion of N terminus of preSPP transit peptide including initial Met triggers processing activity. • The active preSPP deletion mutants no longer possess predicted Hsp70 binding sites. The stromal processing peptidase (SPP) removes transit peptides as precursor proteins enter the chloroplast and different plastid types. SPP is synthesized as a latent, inactive precursor (preSPP) with an atypically long transit peptide. Determinants in the pea (Pisum sativum) SPP transit peptide that regulate mature SPP activation were investigated. Mutational and chemical analyses with protein modifying agents (NEM and APMA) showed a conserved transit peptide Cys-X-Ser/Thr-Cys motif did not inhibit SPP via a “cysteine switch” mechanism through His-X-X-Glu-His site interactions, although cysteines in mature SPP contribute to an active conformation. Significantly, a transit peptide deletion of only the N-terminal 28 amino acids activates SPP located downstream. Short deletions within this region suggest removal of the initial Met plays a pivotal, mechanistic role. Other deletions of ∼30 amino acids along the length of the transit peptide do not individually trigger activity, but larger deletions including Met have an additive effect indicating its removal may be a critical early step during preSPP import. Interestingly, the active preSPP deletion mutants no longer possess predicted Hsp70 binding sites including initial Met, thus Hsp70 interactions may restrict SPP from attaining an active conformation.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Hole Hopping through Cytochrome P450

High-potential iron–oxo species are intermediates in the catalytic cycles of oxygenase enzymes. They can cause heme degradation and irreversible oxidation of nearby amino acids. We have proposed that there are protective mechanisms in which hole hopping from oxidized hemes through tryptophan/tyrosine chains generates a surface-exposed amino-acid oxidant that could be rapidly disarmed by reaction with cellular reductants. In investigations of cytochrome P450 BM 3 , we identified Trp96 as a critical residue that could play such a protective role. This Trp is cation-π paired with Arg398 in 81% of mammalian P450s. Here we report on the effect of the Trp/Arg cation-π interaction on Trp96 formal potentials as well as on electronic coupling strengths between Trp96 and the heme both for wild type cytochrome P450 and selected mutants. Mutation of Arg398 to His, which decreases the Trp96 formal potential, increases Trp-heme electronic coupling; however, surprisingly, the rate of phototriggered electron transfer from a Ru-sensitizer (through Trp96) to the P450 BM 3 heme was unaffected by the Arg398His mutation. We conclude that Trp96 has moved away from Arg398, suggesting that the protective mechanism for P450s with this Trp-Arg pair is conformationally gated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1978

Origins of prokaryotes, eukaryotes, mitochondria, and chloroplasts

A computer branching model is used to analyze cellular evolution. Attention is given to certain key amino acids and nucleotide residues (ferredoxin, 5s ribosomal RNA, and c-type cytochromes) because of their commonality over a wide variety of cell types. Each amino acid or nucleotide residue is a sequence in an inherited biological trait; and the branching method is employed to align sequences so that changes reflect substitution of one residue for another. Based on the computer analysis, the symbiotic theory of cellular evolution is considered the most probable. This theory holds that organelles, e.g., mitochondria and chloroplasts invaded larger bodies, e.g., bacteria, and combined functions to form eucaryotic cells.

Schwartz, R. M.↗

NASA NTRS2006

Laboratory Studies on the Formation of Carbon-Bearing Molecules in Extraterrestrial Environments: From the Gas Phase to the Solid State

A detailed knowledge of the formation of carbon-bearing molecules in interstellar ices and in the gas phase of the interstellar medium is of paramount interest to understand the astrochemical evolution of extraterrestrial environments (1). This research also holds strong implications to comprehend the chemical processing of Solar System environments such as icy planets and their moons together with the atmospheres of planets and their satellites (2). Since the present composition of each interstellar and Solar System environment reflects the matter from which it was formed and the processes which have changed the chemical nature since the origin (solar wind, planetary magnetospheres, cosmic ray exposure, photolysis, chemical reactions), a detailed investigation of the physicochemical mechanisms altering the pristine environment is of paramount importance to grasp the contemporary composition. Once these underlying processes have been unraveled, we can identify those molecules, which belonged to the nascent setting, distinguish molecular species synthesized in a later stage, and predict the imminent chemical evolution of, for instance, molecular clouds. Laboratory experiments under controlled physicochemical conditions (temperature, pressure, chemical composition, high energy components) present ideal tools for simulating the chemical evolution of interstellar and Solar System environments. Here, laboratory experiments can predict where and how (reaction mechanisms; chemicals necessary) in extraterrestrial environments and in the interstellar medium complex, carbon bearing molecules can be formed on interstellar grains and in the gas phase. This paper overviews the experimental setups utilized in our laboratory to mimic the chemical processing of gas phase and solid state (ices) environments. These are a crossed molecular beams machine (3) and a surface scattering setup (4). We also present typical results of each setup (formation of amino acids, aldehydes, epoxides; synthesis of hydrogen terminated carbon chains as precursors to complex PAHs and to carbonaceous dust grains in general; nitriles as precursor to amino acids).

Jamieson, C. S.↗

NASA NTRS2010

Comparison of the Organic Composition of Cometary Samples with Residues Formed from the UV Irradiation of Astrophysical Ice Analogs

The NASA Stardust mission successfully collected material from Comet 81P/Wild 2 [1], including authentic cometary grains [2]. X-ray absorption near-edge structure (XANES) spectroscopy analysis of these samples indicates the presence of oxygen-rich and nitrogen-rich organic materials, which contain a broad variety of functional groups (carbonyls, C=C bonds, aliphatic chains, amines, arnides, etc.) [3]. One component of these organics appears to contain very little aromatic carbon and bears some similarity to the organic residues produced by the irradiation of ices of interstellar/cometary composition, Stardust samples were also recently shown to contain glycine, the smallest biological amino acid [4]. Organic residues produced froth the UV irradiation of astrophysical ice analogs are already known to contain a large suite of organic molecules including amino acids [5-7], amphiphilic compounds (fatty acids) [8], and other complex species. This work presents a comparison between XANES spectra measured from organic residues formed in the laboratory with similar data of cometary samples collected by the Stardust mission

Milam, S. N.↗

NASA NTRS2018

Compound-Specific Carbon Isotope Compositions of Aldehydes and Ketones in the Murchison Meteorite

Compound-specific carbon isotope analysis (delta(exp 13)C) of meteoritic organic compounds can be used to elucidate the abiotic chemical reactions involved in their synthesis. The soluble organic content of the Murchison carbonaceous chondrite has been extensively investigated over the years, with a focus on the origins of amino acids and the potential role of Strecker-cyanohydrin synthesis in the early solar system. Previous delta(exp 13)C investigations have targeted alpha-amino acid and alpha-hydroxy acid Strecker products and reactant HCN; however, delta(exp 13)C values for meteoritic aldehydes and ketones (Strecker precursors) have not yet been reported. As such, the distribution of aldehydes and ketones in the cosmos and their role in prebiotic reactions have not been fully investigated. Here, we have applied an optimized O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine (PFBHA) derivatization procedure to the extraction, identification, and delta(exp 13)C analysis of carbonyl compounds in the Murchison meteorite. A suite of aldehydes and ketones, dominated by acetaldehyde, propionaldehyde, and acetone, were detected in the sample. delta(exp 13)C values, ranging from -10.0(0/00) to +66.4(0/00), were more (exp 13)C-depleted than would be expected for aldehydes and ketones derived from the interstellar medium, based on interstellar (exp 12)C/(exp 13)C ratios. These relatively (exp 13)C-depleted values suggest that chemical processes taking place in asteroid parent bodies (e.g., oxidation of the IOM) may provide a secondary source of aldehydes and ketones in the solar system. Comparisons between delta(exp 13)C compositions of meteoritic aldehydes and ketones and other organic compound classes were used to evaluate potential structural relationships and associated reactions, including Strecker synthesis and alteration-driven chemical pathways.

meteoritic organic compounds↗

NASA NTRS2018

The Diversity of Refractory Organic Material in Comets

Organic matter exists in comets (most notably in 81P/Wild 2 [Stardust], 67P/Churyomov- Gerasimenko (67P/C-G) [Rosetta], chondritic porous IDPS, and UCAMMs) and in primitive carbonaceous chondrites that likely retain some chemistry that reflects an origin in the prenatal cold molecular cloud (Alexander+2017). Heavy isotopic enrichments, 15N/14N and possibly D/H, signify preserved molecular cloud organics. In the cold outer disk, if grains are lofted above the disk mid-plane then organics likely experience significant UV processing (Ciesla+2012). In remote sensing of comet comae, organics in the dust are considered refractory or semirefractory. Semi-refractory organics have limited comae lifetimes and produce distributed sources of molecules (H2CO and CO). Rosetta's close passes of 67P/C-G's nucleus (10-15 km) reveals a distributed source of glycine, methyl amine and ethylamine (Altwegg+2016). Cometary samples and primitive meteorites have two types of organic matter: (1) acid-insoluble organic matter (IOM), which is a macromolecular polymer with a mixture of aromatic and aliphatic moieties, and (2) labile, soluble organics, which includes the amino acids, such as glycine (Stardust, Elsila+2009). Meteoritic IOM is robust, withstanding experimental temperatures of 1200 K (Dobrica+2011, Cody+2008). Nanoglobules are a type of IOM; they have a distinct physical structure, but often share the same chemistry as the other IOM from the same meteorite. Moderate-sized PAHs (20 C-atoms) are detected in Stardust samples (Clemett+2010). Refractory organic IOM is ubiquitous yet has a great diversity of abundances between cometary samples. IOM is in primitive chondrites, 67P/C-G (Rosetta), 81P/Wild 2 (Stardust), 1P/Halley, 26P/Grigg-Skjellerup, UCAMMs, anhydrous IDPs, and in chondritic porous IDPs (CP IDPs) and larger cluster IDPs (e.g., Fray+2016, Fomenkova+94, Busemann+ 09, Dobrica+2011, Dobrica+2012). 81P's refractory organic matter is of two types (De Gregorio+2011): nanoglobules of highly aromatic refractory organic matter and polyaromatic carbonyl-containing organic matter, which is similar to IOM in primitive meteorites and IDPs. Fray+2017 estimate that 50% of carbon in 67P/C-G is in IOM. 67P/C-G's organics appear to lack the soluble organic matter, aliphatic carbon, amino acids, and PAHs (Fray+2016). Other notable aspects of the diversity in IOM in cometary samples are the ranges of atomic ratios of N/C, O/C, and H/C, and the range of isotopic enrichments of 15N/14N and D/H. Aqueous and thermal processing on asteroids changes the balance of soluble to insoluble organics, and may be important for diversifying the range of OM delivered to Earth.

Wooden, Diane↗

DOE OSTI2015

Integrating mRNA and protein sequencing enables the detection and quantitative profiling of natural protein sequence variants of Populus trichocarpa

The availability of next-generation sequencing technologies has rapidly transformed our ability to link genotypes to phenotypes, and as such, promises to facilitate the dissection of genetic contribution to complex traits. Although discoveries of genetic associations will further our understanding of biology, once candidate variants have been identified, investigators are faced with the challenge of characterizing the functional effects on proteins encoded by such genes. Here we show how next-generation RNA sequencing data can be exploited to construct genotype-specific protein sequence databases, which provide a clearer picture of the molecular toolbox underlying cellular and organismal processes and their variation in a natural population. For this study, we used two individual genotypes (DENA-17-3 and VNDL-27-4) from a recent genome wide association (GWA) study of Populus trichocarpa, an obligate outcrosser that exhibits tremendous phenotypic variation across the natural population. This strategy allowed us to comprehensively catalogue proteins containing single amino acid polymorphisms (SAAPs) and insertions and deletions (INDELS). Based on large-scale identification of SAAPs, we profiled the frequency of 128 types of naturally occurring amino acid substitutions, with a subset of SAAPs occurring in regions of the genome having strong polymorphism patterns consistent with recent positive and/or divergent selection. In addition, we were able to explore the diploid landscape of Populus at the proteome-level, allowing the characterization of heterozygous variants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Does aspartic acid racemization constrain the depth limit of the subsurface biosphere?

Previous studies of the subsurface biosphere have deduced average cellular doubling times of hundreds to thousands of years based upon geochemical models. We have directly constrained the in situ average cellular protein turnover or doubling times for metabolically active micro-organisms based on cellular amino acid abundances, D/L values of cellular aspartic acid, and the in vivo aspartic acid racemization rate. Application of this method to planktonic microbial communities collected from deep fractures in South Africa yielded maximum cellular amino acid turnover times of ~89 years for 1 km depth and 27 C and 1 2 years for 3 km depth and 54 C. The latter turnover times are much shorter than previously estimated cellular turnover times based upon geochemical arguments. The aspartic acid racemization rate at higher temperatures yields cellular protein doubling times that are consistent with the survival times of hyperthermophilic strains and predicts that at temperatures of 85 C, cells must replace proteins every couple of days to maintain enzymatic activity. Such a high maintenance requirement may be the principal limit on the abundance of living micro-organisms in the deep, hot subsurface biosphere, as well as a potential limit on their activity. The measurement of the D/L of aspartic acid in biological samples is a potentially powerful tool for deep, fractured continental and oceanic crustal settings where geochemical models of carbon turnover times are poorly constrained. Experimental observations on the racemization rates of aspartic acid in living thermophiles and hyperthermophiles could test this hypothesis. The development of corrections for cell wall peptides and spores will be required, however, to improve the accuracy of these estimates for environmental samples.

Onstott, T. C.↗

NASA NTRS2013

Does Aspartic Acid Racemization Constrain the Depth Limit of the Subsurface Biosphere?

Previous studies of the subsurface biosphere have deduced average cellular doubling times of hundreds to thousands of years based upon geochemical models. We have directly constrained the in situ average cellular protein turnover or doubling times for metabolically active micro-organisms based on cellular amino acid abundances, D/L values of cellular aspartic acid, and the in vivo aspartic acid racemization rate. Application of this method to planktonic microbial communities collected from deep fractures in South Africa yielded maximum cellular amino acid turnover times of approximately 89 years for 1 km depth and 27 C and 1-2 years for 3 km depth and 54 C. The latter turnover times are much shorter than previously estimated cellular turnover times based upon geochemical arguments. The aspartic acid racemization rate at higher temperatures yields cellular protein doubling times that are consistent with the survival times of hyperthermophilic strains and predicts that at temperatures of 85 C, cells must replace proteins every couple of days to maintain enzymatic activity. Such a high maintenance requirement may be the principal limit on the abundance of living micro-organisms in the deep, hot subsurface biosphere, as well as a potential limit on their activity. The measurement of the D/L of aspartic acid in biological samples is a potentially powerful tool for deep, fractured continental and oceanic crustal settings where geochemical models of carbon turnover times are poorly constrained. Experimental observations on the racemization rates of aspartic acid in living thermophiles and hyperthermophiles could test this hypothesis. The development of corrections for cell wall peptides and spores will be required, however, to improve the accuracy of these estimates for environmental samples.

cellular↗