Bacteria and archaea

An enzyme that catalyzes the reduction of A -piperidein-2-carboxylate to piperidine-2-car-boxylate (r-pipecolate) in the catabolism of o-lysine by Pseudomonas putida ATCC12633 is an NADPH-dependent representative of a large family of reductases that are distributed among bacteria and archaea (Muramatsu et al. 2005). It also catalyzes the reduction of A -pyrrolidine-2-carboxylate to L-proline. 

These reductases play a key role both in methanogenesis and in the degradation of phenols that carry several nitro groups, which is discussed further in Chapter 9, Part 5. Although these reductases are typically found in methanogens, they have been encountered in a number of other bacteria and archaea ... 

Robbins, E. I. Bacteria and Archaea in acidic environments and a key to morphological identification. Hydrobiologia 2000,433, 61-89. 

Two original kingdoms first developed from the last universal common ancestor bacteria and archaea. 

Oxidation of Fe(ll) occurs rapidly at low pH but at measureable rates of about 1-5 mmol/L/h in surface waters by chemoautotrophic bacteria and archaea (Nordstrom 2003). 

P-type ATPases from eukaryotes, bacteria, and Archaea catalyse cation uptake and/or efflux driven by ATP hydrolysis. Bacterial P-type ATPases... 

ABC transporters involved in the uptake of siderophores, haem, and vitamin B]2 are widely conserved in bacteria and Archaea (see Figure 10). Very few species lack representatives of the siderophore family transporters. These species are mainly intracellular parasites whose metabolism is closely coupled to the metabolism of their hosts (e.g. mycoplasma), or bacteria with no need for iron (e.g. lactobacilli). In many cases, several systems of this transporter family can be detected in a single species, thus allowing the use of structurally different chelators. Most systems were exclusively identified by sequence data analysis, some were biochemically characterised, and their substrate specificity was determined. However, only very few systems have been studied in detail. At present, the best-characterised ABC transporters of this type are the fhuBCD and the btuCDF systems of E. coli, which might serve as model systems of the siderophore family. Therefore, in the following sections, this report will mainly focus on the components that mediate ferric hydroxamate uptake (fhu) and vitamin B12 uptake (htu). 

In our previous analysis, correlation coefficients were used between the fold distributions in different genomes to construct a distance matrix and a corresponding cluster dendogram (Wolf et al., 1999). This clustering showed significant differences in the fold composition between eukaryotes and prokaryotes (bacteria and archaea) as well as between free-living and parasitic bacteria. 

EFTsNT A UBA-like domain with a clear role outside of ubiquitin binding is found at the N-terminus of EF-Ts proteins. The relationship of this region to genuine UBA domains is well established as there is a structure of full-length EF-Ts available [67]. Nevertheless, this domain is widespread in bacteria and archaea, which obviously lack a proper ubiquitin system. The physiological role of the EFTsNT domain is rather in the binding to the elongation factor EF-Tu, which has no resemblance to ubiquitin. 

Slobodkin AI, Jeanthon C, L Haridon S, et al. 1999a. Dissimilatory reduction of Fe(III) by thermophlic bacteria and archaea in deep subsurface petroleum reservoirs of western Siberia. Curr Microbiol 39 99-102. 

The biological classification schemes for bacteria and archaea are still being developed because of the rapid pace of new discoveries in genomics. The two most important phyla of marine bacteria are the cyanobacteria, which are photosynthetic, and the proteobacteria. The latter include some photosynthetic species, such as the purple photosynthetic bacteria and N2 fixers. Other members of this diverse phylum are the methanotrophs, nitrifiers, hydrogen, sulfur and iron oxidizers, sulfete and sulfur reducers, and various bioluminescent species. 

Finally, it is noteworthy that not all marine organisms are classifiable as POM. Viruses, small bacteria, and archaea can pass through 0.2-p,m filter pores and, thus, are technically part of the DOM. Although these organisms are small (0.2 to 20 x 10 gC/cell for viruses and bacteria, respectively), their high numbers (10 to lO and 10 to 10 cells/L, respectively) cause their collective biomass in seawater to be similar to that of phytoplankton and zooplankton (<2mm) (Table 23.2). The biomass of the archaea and the macrozooplankton (>2 mm) are currently unknown. Nonetheless, these two groups play very important biogeochemical roles as described later. 

Nelson KE, Paulsen IT, Heidelberg JP, et al. Status of genome projects for non-pathogenic bacteria and archaea. Nat Biotechnol 2000 18 1049-54. 

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