Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation.

The microbial cleavage of dimethylsulfoniopropionate (DMSP) generates volatile DMS through the action of DMSP lyases and is important in the global sulfur and carbon cycles. When released into the atmosphere from the oceans, DMS is oxidized, forming cloud condensation nuclei that may influence weather and climate. Six different DMSP lyase genes are found in taxonomically diverse microorganisms, and dddQ is among the most abundant in marine metagenomes. Here, we examine the molecular mechanism of DMSP cleavage by the DMSP lyase, DddQ, from Ruegeria lacuscaerulensis ITI_1157. The structures of DddQ bound to an inhibitory molecule 2-(N-morpholino)ethanesulfonic acid and of DddQ inactivated by a Tyr131Ala mutation and bound to DMSP were solved. DddQ adopts a β-barrel fold structure and contains a Zn 2+ ion and six highly conserved hydrophilic residues (Tyr120, His123, His125, Glu129, Tyr131, and His163) in the active site. Mutational and biochemical analyses indicate that these hydrophilic residues are essential to catalysis. In particular, Tyr131 undergoes a conformational change during catalysis, acting as a base to initiate the β-elimination reaction in DMSP lysis. Moreover, structural analyses and molecular dynamics simulations indicate that two loops over the substratebinding pocket of DddQ can alternate between "open" and "closed" states, serving as a gate for DMSP entry. We also propose a molecular mechanism for DMS production through DMSP cleavage. Our study provides important insight into the mechanism involved in the conversion of DMSP into DMS, which should lead to a better understanding of this globally important biogeochemical reaction.DMSP lyase DddQ | DMSP lyase structure | DMS generation | DMSP cleavage mechanism | marine bacteria T he compatible solute dimethylsulfoniopropionate (DMSP) is produced worldwide in a large amount, ∼10 9 tons per annum, mainly by marine phytoplankton and macroalgae; thus, this compound is a major participant in the global sulfur and carbon cycles (1, 2). Some DMSP is broken down by the algae producing it (3), but it is primarily catabolized by marine bacteria via two pathways, the demethylation pathway and the cleavage pathway (4). In the demethylation pathway, DMSP is demethylated and the methylmercaptopropionate generated is subsequently demethiolated to release methanthiol, providing the marine microbial food web a source of reduced sulfur (4). In the cleavage pathway, DMSP is cleaved by DMSP lyases to generate DMS, an environmentally important gas, and acrylate (or 3-hydroxypropionate) (5). DMS is the major form of biogenic sulfur that enters the atmosphere from the oceans (6). Some 300 Tg of DMS is annually produced by microbial activities, about 10% of which is transferred from oceans to the atmosphere (7,8). DMS in the atmosphere can be photochemically oxidized into DMSO or sulfate aerosols (9), which can scatter solar radiation directly and also form cloud condensation nuclei that influence the reflectivity of clouds and thereby global temperature (9, 10). These s...

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