Research Progress in Ammonia Assimilation and Genetic Evolution in Rumen

doi:10.13560/j.cnki.biotech.bull.1985.2024-0764

Abstract

Abstract:

The shortage of protein feed resources has severely restricted the sustained and stable development of animal husbandry in China. Ruminants possess the special ability to convert non-protein nitrogen into amino acids or proteins. Adding non-protein nitrogen is an effective approach to alleviate protein feed shortages in ruminants, but rumen ammonia assimilation is the key step limiting its utilization efficiency. Therefore, improving the nitrogen assimilation efficiency of ruminants is an important means of alleviating the shortage of protein feed. Ammonia assimilation refers to the process of free ammonia merging into the carbon skeleton to form nitrogen-containing organic compounds. Rumen microorganisms may assimilate free ammonia into microbial protein (MCP), providing 49%-98% of metabolizable protein for ruminants. Rumen ammonia assimilation can be carried out through four pathways: ① the glutamate dehydrogenase (GDH) pathway: ammonia and α-ketoglutarate undergo aminification catalyzed by GDH to produce glutamate; ② the glutamine synthetase-glutamate synthase (GS-GOGAT) pathway: ammonia and glutamate are catalyzed by GS to form glutamine;③ the alanine dehydrogenase (ADH) pathway: alanine can be produced by ammonia and pyruvate through the ADH pathway; ④ the asparagine synthetase (AS) pathway: aspartate and ammonia can form asparagine through the AS pathway. This article explores the process of ammonia assimilation pathway reaction in rumen microorganisms and reviews these four ammonia assimilation pathways of rumen microbes, their key enzymes, microorganisms involved, and influencing factors. By constructing phylogenetic trees to explain the evolutionary relationships of key genes, theoretical support for the utilization of ammonia nitrogen in ruminants is provided.

Key words: ruminants, non-protein nitrogen, ammonia assimilation pathway, GDH pathways, GS-GOGAT pathways

WANG Tong, XIAO Han-jie, XIE Hao-jiong, ZHANG Li-shen, YAO Xiao-liang, YAN Hui, JI Shou-kun. Research Progress in Ammonia Assimilation and Genetic Evolution in Rumen[J]. Biotechnology Bulletin, 2025, 41(2): 40-50.

Figures/Tables 11

Fig. 1 Pathway of GDH

Fig. 2 Structure of GDHA: Cartoon representation of hexameric and subunit GDH structure. The structure is built based on the whole genome of B. fibrisolvens using the AlphaFold3 platform (NCBI GenBank: GCA_037113525.1). B: Schematic diagram depicting conformational change in GDH structure upon substrate and coenzyme binding

Fig. 3 Pathway of GS-GOGAT

Fig. 4 Multimeric structures of the three types of GSThe structures are from the PDB database, with serial number 5ZLP, 7v4i, and 8TGE, respectively

Fig. 5 Structure of GOGATA: Schematic diagram of Fd-GOGAT structure, from PDB (1 LLZ). B: Schematic diagram of NADPH-GOGAT structure. Structure based on B. fibrisolvens genome data (NCBI GenBank: GCA_037113525.1), predicted by AlphaFold3

Fig. 6 Pathway of ADH

Fig. 7 Structure of ADHA: The structural diagram of ADH hexamer, with different colors representing different subunits. B: The structural diagram of ADH monomer, where the ball-and-stick model indicates NAD+ and the red hexagon indicates pyruvate. The structure in the figure is based on the whole genome data of B. fragilis, and protein structure prediction was conducted using the AlphaFold3 platform (NCBI GenBank: GCA_016889925.1)

Fig. 8 Pathway of AS

Fig. 9 Structure of ASA: The structural diagram of AS-B monomer. B: Structure diagram of AS-B dimer. C: Structure diagram of AS-A dimer. The structures are all built based on the whole genome data of B. fibrisolvens (NCBI GenBank: GCA_037113525.1) using the AlphaFold3 platform

Fig. 10 Relationship diagram of four ammonia assimilation pathways in rumen bacteria

Fig. 11 Phylogenetic trees of 16S rRNA and key genes in the ammonia assimilation pathwayA: 16S rRNA phylogenetic tree of 31 rumen bacterial strains. B: Phylogenetic tree of gdhA gene (GDH pathway). C: Phylogenetic trees of glnA gene (GS-GOGAT pathway). D: Phylogenetic tree of ald gene (ADH pathway); E and F is phylogenetic trees of asnA and asnB genes, respectively (AS pathway). The dashed lines in Fig. B-F indicate the location of genotyping. Homologous genes were retrieved using HMMER. Trees are constructed using MEGA 11 with maximum likelihood method. Bootstrap values are 100

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