Microbial D-amino acids and marine carbon storage

Science China Earth Sciences - Tập 59 - Trang 17-24 - 2015
ZiLian Zhang1, Qiang Zheng1, NianZhi Jiao1
1State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China

Tóm tắt

In nature, there are two conformational types of amino acids: L- and D-isomers. The L-amino acids are the predominant form and are used mainly for protein synthesis, while the D-amino acids are few in quantity but more diverse in terms of their biological functions. D-amino acids are produced by many marine microbes, which are important players in carbon and energy cycles in the ocean. As the major constituent of the marine organic carbon pool, D-amino acids can persist in the water column for a long time before being further transformed by chemical or biological processes or transported through physical processes (such as absorption and aggregation). This article reviews the microbial synthesis of D-amino acids, their physiological function and metabolism in microbes, and the contribution of D-amino acids as a carbon source to the oceanic carbon reservoir.

Tài liệu tham khảo

Abe H, Okuma E, Amano H, Noda H, Watanabe K. 1999. Role of free d- and l-alanine in the Japanese mitten crab Eriocheir japonicus to intracellular osmoregulation during downstream spawning migration. Comp Biochem Phys A, 123: 55–59 Auclair J, Patton R. 1950. On the occurrence of D-alanine in the haemolymph of the milkweed bug, oncopeltus fasciatus. Rev Can Biol, 9: 3 Azam F, Malfatti F. 2007. Microbial structuring of marine ecosystems. Nature Rev Microbiol, 5: 782–791 Barja I, Núñez L. 1999. Microcalorimetric measurements of the influence of glucose concentration on microbial activity in soils. Soil Biol Biochem, 31: 441–447 Brodowski S, Amelung W, Lobe I, Du Preez C C. 2005. Losses and biogeochemical cycling of soil organic nitrogen with prolonged arable cropping in the South African Highveld—Evidence from D- and L-amino acids. Biogeochemistry, 71: 17–42 Brown M, Lauro F, Demaere M, Muir L, Wilkins D, Thomas T, Riddle M, Fuhrman J, Andrews-Pfannkoch C, Hoffman J. 2012. Global biogeography of SAR11 marine bacteria. Mol Syst Biol, 8: 595 Brückner H, Westhauser T. 2003. Chromatographic determination of L-and D-amino acids in plants. Amino Acids, 24: 43–55 Dauwe B, Middelburg J J. 1998. Amino acids and hexosamines as indicators of organic matter degradation state in North Sea sediments. Limnol Oceanogr, 43: 782–798 Delfosse V, Girard E, Birck C, Delmarcelle M, Delarue M, Poch O, Schultz P, Mayer C. 2009. Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family. PLoS One, 4: e4712 DeLong E F. 1992. Archaea in coastal marine environments. Proc Natl Acad Sci USA, 89: 5685–5689 Eichinger M, Poggiale J C, Van Wambeke F, Lefevre D, Sempere R. 2006. Modelling DOC assimilation and bacterial growth efficiency in biodegradation experiments: A case study in the Northeast Atlantic Ocean. Aquat Microbial Ecol, 43: 139–151 Fernandes L, Garg A, Borole D V. 2014. Amino acid biogeochemistry and bacterial contribution to sediment organic matter along the western margin of the Bay of Bengal. Deep-Sea Res Part I: Oceanogr Res Pap, 83: 81–92 Flemming H C, Wingender J. 2010. The biofilm matrix. Nature Rev Microbiol, 8: 623–633 Forsum O, Svennerstam H, Ganeteg U, Näsholm T. 2008. Capacities and constraints of amino acid utilization in Arabidopsis. New Phytol, 179: 1058–1069 Gehlen M. 2006. Reconciling surface ocean productivity, export fluxes and sediment composition in a global biogeochemical ocean model. Biogeosciences, 3: 521–537 Giovannoni S, Rappé M. 2000. Evolution, diversity, and molecular ecology of marine prokaryotes. In: Kirchman D, ed. Microbial Ecology of the Oceans. New York: Wiley. 47–84 Gördes D, Kolukisaoglu Ü, Thurow K. 2011. Uptake and conversion of D-amino acids in Arabidopsis thaliana. Amino Acids, 40: 553–563 Halvorson H O, Spiegelman S. 1952. The inhibition of enzyme formation by amino acid analogues. J Bacteriol, 64: 207–221 Herndl G J, Reinthaler T, Teira E, Aken H M V, Veth C, Pernthaler A, Pernthaler J. 2005. Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean. Appl Environ Microbiol, 72: 2303–2309 Hertkorn N, Benner R, Frommberger M, Schmitt-Kopplin P, Witt M, Kaiser K, Kettrup A, Hedges J I. 2006. Characterization of a major refractory component of marine dissolved organic matter. Geochim Cosmochim Acta, 70: 2990–3010 Hill P W, Quilliam R S, DeLuca T H, Farrar J, Farrell M, Roberts P, Newsham K K, Hopkins D W, Bardgett R D, Jones D L. 2011. Acquisition and assimilation of nitrogen as peptide-bound and D-enantiomers of amino acids by wheat. PLoS One, 6: e19220 Hills G. 1949. Chemical factors in the germination of spore-bearing aerobes. The effects of amino-acids on the germination of Bacillus anthracis, with some observations on the relation of optical form to biological activity. Biochem J, 45: 363 Hochbaum A I, Kolodkin-Gal I, Foulston L, Kolter R, Aizenberg J, Losick R. 2011. Inhibitory effects of D-amino acids on Staphylococcus aureus biofilm development. J Bacteriol, 193: 5616–5622 Huang Y, Nishikawa T, Satoh K, Iwata T, Fukushima T, Homma H, Imai K. 1998. Urinary excretion of D-serine in human: Comparison of different ages and species. Biol Pharm Bull, 21: 156 Jensen P, Fenical W. 1995. The relative abundance and seawater requirements of Gram-positive bacteria in near-shore tropical marine samples. Microb Ecol, 29: 249–257 Jiao N, Herndl G J, Hansell D A, Benner R, Kattner G, Wilhelm S W, Kirchman D L, Weinbauer M G, Luo T, Chen F, Azam F. 2010. Microbial production of recalcitrant dissolved organic matter: Long-term carbon storage in the global ocean. Nature Rev Microbiol, 8: 593–599 Jørgensen N O G, Stepanaukas R, Pedersen A G U, Hansen M, Nybroe O. 2003. Occurrence and degradation of peptidoglycan in aquatic environments. FEMS Microbiol Ecol, 46: 269–280 Jørgensen N O G, Middelboe M. 2006. Occurrence and bacterial cycling of D-amino acid isomers in an estuarine environment. Biogeochemistry, 81: 77–94 Kaiser K, Benner R. 2008. Major bacterial contribution to the ocean reservoir of detrital organic carbon and nitrogen. Limnol Oceanogr, 53: 99–112 Kandler O, König H. 1978. Chemical composition of the peptidoglycanfree cell walls of methanogenic bacteria. Arch Microbiol, 118: 141–152 Kandler O, König H. 1998. Cell wall polymers in Archaea (Archaebacteria). Cell Mol Life Sci, 54: 305–308 Karatan E, Watnick P. 2009. Signals, regulatory networks, and materials that build and break bacterial biofilms. Microbiol Mol Biol Rev, 73: 310–347 Karner M B, DeLong E F, Karl D M. 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature, 409: 507–510 Kawai Y, Ishii Y, Arakawa K, Uemura K, Saitoh B, Nishimura J, Kitazawa H, Yamazaki Y, Tateno Y, Itoh T. 2004. Structural and functional differences in two cyclic bacteriocins with the same sequences produced by lactobacilli. Appl Environ Microbiol, 70: 2906–2911 Kawasaki N, Benner R. 2006. Bacterial release of dissolved organic matter during cell growth and decline: Molecular origin and composition. Limnol Oceanogr, 51: 2170–2180 Kim P M, Duan X, Huang A S, Liu C Y, Ming G L, Song H, Snyder S H. 2010. Aspartate racemase, generating neuronal D-aspartate, regulates adult neurogenesis. Proc Natl Acad Sci USA, 107: 3175–3179 Kolodkin-Gal I, Romero D, Cao S, Clardy J, Kolter R, Losick R. 2010. D-amino acids trigger biofilm disassembly. Science, 328: 627–629 Könneke M, Bernhard A E, José R, Walker C B, Waterbury J B, Stahl D A. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature, 437: 543–546 Lam H, Oh D C, Cava F, Takacs C N, Clardy J, de Pedro M A, Waldor M K. 2009. D-Amino acids govern stationary phase cell wall remodeling in bacteria. Science, 325: 1552–1555 Lee C, Bada J L. 1977. Dissolved amino acids in the equatorial Pacific, the Sargasso Sea, and Biscayne Bay. Limnol Oceanogr, 22: 502–510 Li C, Yao X, Lu C D. 2009. Regulation of the dauBAR operon and characterization of D-amino acid dehydrogenase DauA in arginine and lysine catabolism of Pseudomonas aeruginosa PAO1. Microbiology, 156: 60–71 Lomstein B A, Jorgensen B B, Schubert C J, Niggemann J. 2006. Amino acid biogeo- and stereochemistry in coastal Chilean sediments. Geochim Cosmochim Acta, 70: 2970–2989 Matsumoto M, Homma H, Long Z, Imai K, Iida T, Maruyama T, Aikawa Y, Endo I, Yohda M. 1999. Occurrence of free D-amino acids and aspartate racemases in hyperthermophilic Archaea. J Bacteriol, 181: 6560–6563 McCarthy M D, Hedges J I, Benner R. 1998. Major bacterial contribution to marine dissolved organic nitrogen. Science, 281: 231–234 Miyoshi Y, Konno R, Sasabe J, Ueno K, Tojo Y, Mita M, Aiso S, Hamase K. 2012. Alteration of intrinsic amounts of D-serine in the mice lacking serine racemase and D-amino acid oxidase. Amino acids, 43: 1919–1931 Moriarty D, Hayward A. 1982. Ultrastructure of bacteria and the proportion of Gram-negative bacteria in marine sediments. Microb Ecol, 8: 1–14 Morikawa M, Daido H, Takao T, Murata S, Shimonishi Y, Imanaka T. 1993. A new lipopeptide biosurfactant produced by Arthrobacter sp. strain MIS38. J Bacteriol, 175: 6459–6466 Nagata T, Meon B, Kirchman D. 2003. Microbial degradation of peptidoglycan in seawater. Limnol Oceanogr, 48: 745–754 Nagata Y, Tanaka K, Iida T, Kera Y, Yamada R H, Nakajima Y, Fujiwara T, Fukumori Y, Yamanaka T, Koga Y. 1999. Occurrence of D-amino acids in a few archaea and dehydrogenase activities in hyperthermophile Pyrobaculum islandicum. Biochim Biophys Acta, 1435: 160–166 Ogawa H, Tanoue E. 2003. Dissolved organic matter in oceanic waters. J Oceanogr, 59: 129–147 Ohnishi M, Saito M, Wakabayashi S, Ishizuka M, Nishimura K, Nagata Y, Kasai S. 2008. Purification and characterization of serine racemase from a hyperthermophilic archaeon, Pyrobaculum islandicum. J Bacteriol, 190: 1359–1365 Pedersen A-GU, Thomsen T R, Lomstein B A, Jørgensen N O G. 2001. Bacterial influence on amino acid enantiomerization in a coastal marine sediment. Limnol Oceanogr, 46: 1358–1369 Ravenschlag K, Sahm K, Amann R. 2001. Quantitative molecular analysis of the microbial community in marine Arctic sediments (Svalbard). Appl Environ Microbiol, 67: 387–395 Reeburgh W S. 1997. Figures summarizing the global cycles of biogeochemically important elements. Bull Ecol Soc Am, 78: 260–267 Rydon H. 1947. D-amino acids in microbiological chemistry. Biochem J, 41: xxxvi Schleifer K H, Kandler O. 1972. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev, 36: 407 Snyder S H, Kim P M. 2000. D-amino acids as putative neurotransmitters: Focus on D-serine. Neurochem Res, 25: 553–560 Vollmer W, Blanot D, De Pedro M A. 2008. Peptidoglycan structure and architecture. FEMS Microbiol Rev, 32: 149–167 Xu H J, Liu Y. 2011. Reduced microbial attachment by D-amino acid-inhibited AI-2 and EPS production. Water Res, 45: 5796–5804 Yokoyama T, Kan-no N, Ogata T, Kotaki Y, Sato M, Nagahisa E. 2003. Presence of free D-amino acids in microalgae. Biosci Biotechnol Biochem, 67: 388 Yoshimura T, Esak N. 2003. Amino acid racemases: Functions and mechanisms. J Biosci Bioeng, 96: 103–109 Zhang G, Sun H J. 2014. Racemization in reverse: Evidence that D-amino acid toxicity on earth is controlled by bacteria with racemases. PLoS One, 9: e92101 Zhang Y, Sintes E, Chen J, Dai M, Jiao N, Herndl G J. 2009. Role of mesoscale cyclonic eddies in the distribution and activity of Archaea and Bacteria in the South China Sea. Aquat Microb Ecol, 56: 65–79 Zhang Z, Li Z, Jiao N. 2014. Effect of D-amino acids of the EPS production and cell aggregation of Alteromonas macleodii stain JL2069. Curr Microbiol, 68: 751–755 Zhuang R, Chen H, Yao J, Li Z, Burnet J E, Choi M M F. 2011. Impact of beta-cypermethrin on soil microbial community associated with its bioavailability: A combined study by isothermal microcalorimetry and enzyme assay techniques. J Hazard Mater, 189: 323–328 Zobell C E. 1946. Marine Microbiology, A monograph on Hydrobacteriology. Waltham: Chronica Botanica Press