New insight into the catalytic properties of rice sucrose synthase

Natural variation of WBR7 confers rice high yield and quality by modulating sucrose supply in sink organs

Grain chalkiness is an undesirable trait that negatively regulates grain yield and quality in rice. However, the regulatory mechanism underlying chalkiness is complex and remains unclear. We identified a positive regulator of white-belly rate (WBR). The WBR7 gene encodes sucrose synthase 3 (SUS3). A weak functional allele of WBR7 is beneficial in increasing grain yield and quality. During the domestication of indica rice, a functional G/A variation in the coding region of WBR7 resulted in an E541K amino acid substitution in the GT-4 glycosyltransferase domain, leading to a significant decrease in decomposition activity of WBR7A (allele in cultivar Jin23B) compared with WBR7G (allele in cultivar Beilu130). The NIL(J23B) and knockout line NIL(BL130)KO exhibited lower WBR7 decomposition activity than that of NIL(BL130) and NIL(J23B)COM, resulting in less sucrose decomposition and metabolism in the conducting organs. This caused more sucrose transportation to the endosperm, enhancing the synthesis of storage components in the endosperm and leading to decreased WBR. More sucrose was also transported to the anthers, providing sufficient substrate and energy supply for pollen maturation and germination, ultimately leading to an increase rate of seed setting and increased grain yield. Our findings elucidate a mechanism for enhancing rice yield and quality by modulating sucrose metabolism and allocation, and provides a valuable allele for improved rice quality.

Multi-omics analyses reveal the mechanisms underlying the responses of Casuarina equisetifolia ssp. incana to seawater atomization and encroachment stress

Casuarina equisetifolia trees are used as windbreaks in subtropical and tropical coastal zones, while C. equisetifolia windbreak forests can be degraded by seawater atomization (SA) and seawater encroachment (SE). To investigate the mechanisms underlying the response of C. equisetifolia to SA and SE stress, the transcriptome and metabolome of C. equisetifolia seedlings treated with control, SA, and SE treatments were analyzed. We identified 737, 3232, 3138, and 3899 differentially expressed genes (SA and SE for 2 and 24 h), and 46, 66, 62, and 65 differentially accumulated metabolites (SA and SE for 12 and 24 h). The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that SA and SE stress significantly altered the expression of genes related to plant hormone signal transduction, plant-pathogen interaction, and starch and sucrose metabolism pathways. The accumulation of metabolites associated with the biosynthetic pathways of phenylpropanoid and amino acids, as well as starch and sucrose metabolism, and glycolysis/gluconeogenesis were significantly altered in C. equisetifolia subjected to SA and SE stress. In conclusion, C. equisetifolia responds to SA and SE stress by regulating plant hormone signal transduction, plant-pathogen interaction, biosynthesis of phenylpropanoid and amino acids, starch and sucrose metabolism, and glycolysis/gluconeogenesis pathways. Compared with SA stress, C. equisetifolia had a stronger perception and response to SE stress, which required more genes and metabolites to be regulated. This study enhances our understandings of how C. equisetifolia responds to two types of seawater stresses at transcriptional and metabolic levels. It also offers a theoretical framework for effective coastal vegetation management in tropical and subtropical regions.

Whole-Genome Resequencing Identifies SNPs in Sucrose Synthase and Sugar Transporter Genes Associated with Sweetness in Coconut

Coconut (Cocos nucifera L.) is an important agricultural commodity with substantial economic and nutritional value, widely used for various products, including coconut water. The sweetness is an important quality trait of coconut water, which is influenced by genetic and environmental factors. In this study, we utilized next-generation sequencing to identify genetic variations in the coconut genome associated with the sweetness of coconut water. Whole-genome resequencing of 49 coconut accessions, including diverse germplasm and an F2 population of 81 individuals, revealed ~27 M SNPs and ~1.5 M InDels. Sugar content measured by °Bx was highly variable across all accessions tested, with dwarf varieties generally sweeter. A comprehensive analysis of the sugar profiles revealed that sucrose was the major sugar contributing to sweetness. Allele mining of the 148 genes involved in sugar metabolism and transport and genotype-phenotype association tests revealed two significant SNPs in the hexose carrier protein (Cnu01G018720) and sucrose synthase (Cnu09G011120) genes associated with the higher sugar content in both the germplasm and F2 populations. This research provides valuable insights into the genetic basis of coconut sweetness and offers molecular markers for breeding programs aimed at improving coconut water quality. The identified variants can improve the selection process in breeding high-quality sweet coconut varieties and thus support the economic sustainability of coconut cultivation.

Current perspectives on the regulatory mechanisms of sucrose accumulation in sugarcane

Sugars transported from leaves (source) to stems (sink) energize cell growth, elongation, and maintenance. which are regulated by a variety of genes. This review reflects progress and prospects in the regulatory mechanism for maximum sucrose accumulation, including the role of sucrose metabolizing enzymes, sugar transporters and the elucidation of post-transcriptional control of sucrose-induced regulation of translation (SIRT) in the accumulation of sucrose. The current review suggests that SIRT is emerging as a significant mechanism controlling Scbzip44 activities in response to endogenous sugar signals (via the negative feedback mechanism). Sucrose-controlled upstream open reading frame (SC-uORF) exists at the 5' leader region of Scbzip44's main ORF, which inhibits sucrose accumulation through post-transcriptional regulatory mechanisms. Sucrose transporters (SWEET1a/4a/4b/13c, TST, SUT1, SUT4 and SUT5) are crucial for sucrose translocation from source to sink. Particularly, SWEET13c was found to be a major contributor to the efflux in the transportation of stems. Tonoplast sugar transporters (TSTs), which import sucrose into the vacuole, suggest their tissue-specific role from source to sink. Sucrose cleavage has generally been linked with invertase isozymes, whereas sucrose synthase (SuSy)-catalyzed metabolism has been associated with biosynthetic processes such as UDP-Glc, cellulose, hemicellulose and other polymers. However, other two key sucrose-metabolizing enzymes, such as sucrose-6-phosphate phosphohydrolase (S6PP) and sucrose phosphate synthase (SPS) isoforms, have been linked with sucrose biosynthesis. These findings suggest that manipulation of genes, such as overexpression of SPS genes and sucrose transporter genes, silencing of the SC-uORF of Scbzip44 (removing the 5' leader region of the main ORF that is called SIRT-Insensitive) and downregulation of the invertase genes, may lead to maximum sucrose accumulation. This review provides an overview of sugarcane sucrose-regulating systems and baseline information for the development of cultivars with higher sucrose accumulation.

Meta-QTL and haplo-pheno analysis reveal superior haplotype combinations associated with low grain chalkiness under high temperature in rice

Chalk, an undesirable grain quality trait in rice, is primarily formed due to high temperatures during the grain-filling process. Owing to the disordered starch granule structure, air spaces and low amylose content, chalky grains are easily breakable during milling thereby lowering head rice recovery and its market price. Availability of multiple QTLs associated with grain chalkiness and associated attributes, provided us an opportunity to perform a meta-analysis and identify candidate genes and their alleles contributing to enhanced grain quality. From the 403 previously reported QTLs, 64 Meta-QTLs encompassing 5262 non-redundant genes were identified. MQTL analysis reduced the genetic and physical intervals and nearly 73% meta-QTLs were narrower than 5cM and 2Mb, revealing the hotspot genomic regions. By investigating expression profiles of 5262 genes in previously published datasets, 49 candidate genes were shortlisted on the basis of their differential regulation in at least two of the datasets. We identified non-synonymous allelic variations and haplotypes in 39 candidate genes across the 3K rice genome panel. Further, we phenotyped a subset panel of 60 rice accessions by exposing them to high temperature stress under natural field conditions over two Rabi cropping seasons. Haplo-pheno analysis uncovered haplotype combinations of two starch synthesis genes, GBSSI and SSIIa, significantly contributing towards the formation of grain chalk in rice. We, therefore, report not only markers and pre-breeding material, but also propose superior haplotype combinations which can be introduced using either marker-assisted breeding or CRISPR-Cas based prime editing to generate elite rice varieties with low grain chalkiness and high HRY traits.

iTRAQ-based proteomic analysis of heteromorphic leaves reveals eco-adaptability of Populus euphratica Oliv

BACKGROUND

Heterophylly is regard as adaptation to different environments in plant, and Populus euphratica is an important heterophyllous woody plant. However, information on its molecular mechanism in eco-adaptability remains obscure.

RESULTS

In this research, proteins were identified by isobaric tags for relative and absolute quantitation (iTRAQ) technology in lanceolate, ovate, and dentate broad-ovate leaves from adult P. euphratica trees, respectively. Besides, chlorophyll content, net photosynthetic rate, stomatal conductance, transpiration rate and peroxidase activity in these heteromorphic leaves were investigated. A total number of 2,689 proteins were detected in the heteromorphic leaves, of which 56, 73, and 222 differential abundance proteins (DAPs) were determined in ovate/lanceolate, dentate broad-ovate/lanceolate, and dentate broad-ovate/ovate comparison groups. Bioinformatics analysis suggested these altered proteins related to photosynthesis, stress tolerance, respiration and primary metabolism accumulated in dentate broad-ovate and ovate leaves, which were consistent with the results of physiological parameters and Real-time Quantitative PCR experiments.

CONCLUSION

This research demonstrated the mechanism of the differential abundance proteins in providing an optimal strategy of resource utilization and survival for P. euphratica, that could offer clues for further investigations into eco-adaptability of heterophyllous woody plants.

Molecular identification and expression analysis of five sucrose synthase genes in Sorghum Bicolor

In higher plants, sucrose synthase (Susy, EC 2.4.1.13) as an enzyme with a core function, involved in the synthesis and breakdown of sugars, and plays an important role in growth and metabolism. Although, the different genes encoding Susy isozyme proteins have been cloned and functionally verified in several plant species, to date detailed information about the Susy genes is lacking in Sorghum. Here, we demonstrated the identification of five novel Susy genes from the sorghum genome database. Sequence, structure and phylogenetic analyses of these five SbSusy genes revealed evolutionary conservation through Susy gene family members across Sorghum and other crop plants. The expression of sorghum Susy genes was investigated via transcriptome database in various developmental stages and different tissues. Further qRT-PCR was performed to reveal the induction of SbSusy genes under salt, drought and sugar induction. The results indicated that all Susy genes were differentially expressed in various tissues and highly associated with sucrose metabolism. This study shows a theoretical reference of Susy genes in Sorghum, which provides new insights for the knowledge of the evolution relationships, and basic information to help clarify the molecular mechanism of Susy synthase genes in Sorghum.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01166-8.

Mitochondria: Key Organelles Accelerating Cell Wall Material Accumulation in Juice Sacs of Pummelo (Citrus grandis L. Osbeck) Fruits during Postharvest Storage

Granulation is a physiological disorder of juice sacs in citrus fruits, which develops through secondary cell wall formation. However, the synergistic changes in the cytoplasm of juice sac cells remain largely unknown. This study investigated the dynamic ultrastructure of juice sacs of “Guanxi” pummelo fruits by transmission electron microscopy and determined their cell wall material, soluble sugar, and organic acid contents. The results showed that lignin and hemicellulose are accumulated in juice sacs isolated from dorsal vascular bundles, while lignin and cellulose contribute to the granulation of juice sacs isolated from septal vascular bundles. The significant differences in lignin, cellulose, and hemicellulose contents between the two types of juice sacs began to be observed at 30 days of storage. Fructose levels were elevated in juice sacs isolated from the dorsal vascular bundles from 10 to 60 days. Sucrose contents significantly decreased in juice sacs isolated from the septal vascular bundles from 30 to 60 days. Meanwhile glucose, citric acid, and malic acid contents exhibited no apparent changes in both types of juice sacs. Based on the comprehensive analysis of the ultrastructure of both types of juice sacs, it was clearly found that plasma membrane ruptures induce cell wall material synthesis in intracellular spaces; however, cell wall substance contents did not significantly increase until the number of mitochondria sharply increased. In particular, sucrose contents began to decrease significantly just after the mitochondria amount largely increased in juice sacs isolated from the septal vascular bundles, indicating that mitochondria play a key role in regulating carbon source sugar partitioning for cell wall component synthesis.

Consuming Different Structural Parts of Bamboo Induce Gut Microbiome Changes in Captive Giant Pandas

Giant pandas consume different structural parts of bamboo (shoots, leaves and culms) during different seasons. Previous research showed different bamboo parts have varying nutritional content and that a long-term diet consisting of a single part of bamboo resulted in remarkable metabolic changes within captive giant pandas. However, the effects on the gut microbiome of giant pandas, as a result of a single bamboo part diet, have not been investigated. Here, we evaluated the changes in gut microbial communities based on single bamboo part diets and their potential implications by using 16S rRNA gene-based amplicon sequencing and metagenome shotgun sequencing. We found that the composition and function of the gut microbiome from captive giant pandas fed exclusively culms were significantly different from that of individuals fed shoots or leaves. During the culm feeding period, the gut microbiome showed strongest digestive capabilities for cellulose, hemicellulose and starch, and had the highest potential abilities for the biosynthesis of bile acids, fatty acids and amino acids. This suggests the microbiome aids in breaking down culm, which is more difficult for giant pandas to digest, as a means to compensate for the nutrient poor content of the culm. Genes related to fatty acid metabolism and tricarboxylic acid cycle enzymes were more abundant during the leaf stage diet than that in the shoot and culm stages. Thus, the microbiome may help giant pandas, which typically have low lipase levels, with fat digestion. These results illustrate that adaptive changes in the gut microbiome community and function may be an important mechanism to aid giant panda digestion when consuming different structural parts of bamboo.

Mutation of UDP-glucose binding motif residues lead to increased affinity for ADP-glucose in sugarcane sucrose phosphate synthase

Plant sucrose-phosphate synthase (SPS) contains a glycosyltransferase domain, which specifically catalyzes reactions with the nucleotide sugar uridine diphosphate glucose (UDP-G) as a donor substrate. Unlike plant SPS, bacterial SPS is predicted to bind other nucleotide sugars, such as adenosine diphosphate glucose (ADP-G). This study aimed to identify the UDP-G binding site of sugarcane (Saccharum officinarum) SPS (SoSPS1) and to improve its affinity for ADP-G by site-directed mutagenesis. To achieve targeted mutagenesis, amino acid distribution and comparative modeling studies were performed, followed by site-directed mutagenesis of SoSPS1 in the putative UDP-G binding motif. The N-terminal deletion of SoSPS1 (∆N-SoSPS1) was used for enzymatic analysis. The results showed that mutations in the R-X₄-K, E-X₇-E, and H-X₅-V motifs significantly affect UDP-G and ADP-G binding. Mutations at R496 and K501 severely attenuate the affinity for UDP-G. Additionally, alanine substitutions at E591 and V570 decreased the UDP-G affinity but remarkably increased its ADP-G affinity. The R-X₄-K motif plays a crucial role in the UDP-G binding site and catalytic activity of plant SPS; thus, its alteration to other amino acids was not viable. The E-X₇-E and H-X₅-V motifs may bind to the nucleotide glucose substrate, indicating that these motifs are involved in substrate specificity. These results agree with substrate docking simulations at the mutated residue positions, supporting the experimental results. These results demonstrate that mutation of E591 and V570 severely attenuated the UDP-G affinity, while retaining its activity against ADP-G, offering strategic insights into increasing sucrose synthesis and plant growth.

Phosphoproteomic Profiling Reveals Early Salt-Responsive Mechanisms in Two Foxtail Millet Cultivars

Excess soluble salts in saline soils are harmful to most plants. Understanding the biochemical responses to salts in plants and studying the salt tolerance-associated genetic resources in nature will contribute to the improvement of salt tolerance in crops. As an emerging model crop, foxtail millet (Setaria italica L.) has been regarded as a novel species for stress resistance investigation. Here, the dynamic proteomic and phosphoproteomic profiling of two foxtail millet varieties of An04 and Yugu2 with contrasting salt tolerance characteristics were investigated under salt stress. In total, 10,366 sites representing to 2,862 proteins were detected and quantified. There were 759 and 990 sites corresponding to 484 and 633 proteins identified under salinity in An04 and Yugu2, respectively, and 1,264 and 1,131 phosphorylation sites corresponding to 789 and 731 proteins were identified between these two varieties before and after salt stress, respectively. The differentially-regulated phosphoproteins (DRPPs) were mainly involved in signal transduction, regulation of gene expression, translation, ion transport, and metabolism processes. Yugu2 possessed signal perception and transduction capabilities more rapidly and had a more intense response compared with An04 upon salinity. The sucrose metabolism pathway, in particularly, might play a vital role in salt response in foxtail millet, which not only provides UDP-glucose for the cellulose synthesis and energy production, but also promotes flavonoid related synthesis to enhance the salt tolerance ability. Over-expressing the phospho-mimic sucrose synthase (SuS) (SuS ^S10D ) in soybean roots enhanced salt tolerance compared with over-expressing SuS lines. The knowledge of this research will shed light on elucidating the mechanisms of salt response, and pave the way for crop varieties innovation and cultivation under salinity and stresses.

Split application enhances sweetpotato starch production by regulating the conversion of sucrose to starch under reduced nitrogen supply

Split application could improve nitrogen (N) uptake and increase sweetpotato yields under reduced N supply; however, little is known about how it affects the process of starch production in storage roots. An experiment was conducted to determine the effects of three N management strategies [conventional basal N management; 80% of the conventional N rate applied as a basal fertilizer; 80% of the conventional N rate equally split at transplanting and 35 days after transplanting] on starch accumulation, enzyme activity and genes expression in the conversion of sucrose to starch and the relationships among them. The results showed that, compared with conventional basal N management, split application decreased sucrose accumulation by 11.78%, but increased starch accumulation by 11.12% through improving the starch accumulation rate under reduced N supply. The ratio of sucrose synthetase to sucrose phosphate synthase, the enzymatic activity of ADP-glucose pyrophosphorylase (AGPP), starch synthase, and the expression of their corresponding genes were promoted by split application under reduced N supply and were positively correlated with starch accumulation rate. AGPP is the rate-limiting enzyme in starch synthesis in storage roots under different N management strategies. These results indicate that starch accumulation was enhanced by split application through regulating the activity and gene expression of key enzymes involved in the conversion of sucrose to starch under reduced N supply.

Down-Regulating Cucumber Sucrose Synthase 4 (CsSUS4) Suppresses the Growth and Development of Flowers and Fruits

Sucrose synthase (SUS), which catalyzes the reversible conversion of sucrose and uridine diphosphate (UDP) into fructose and UDP-glucose, is a key enzyme in sucrose metabolism in higher plants. In this study, we used reverse genetic approaches and carbohydrate analysis to investigate the role of cucumber sucrose synthase gene 4 (CsSUS4) in the growth and development of sink organs. Transcript analyses showed that CsSUS4 was predominantly expressed in sink organs, particularly in flowers, fruits and roots, and that CsSUS4 protein was localized to companion cells and phloem parenchyma cells. Down-regulation of CsSUS4 expression resulted in a decrease in SUS activity in conjunction with lower hexose, starch and cellulose contents in fruits, and led to an overall reduction in the size and weight of flowers and fruits. Furthermore, CsSUS4 overexpression (OE) lines exhibited increased carbohydrate content, and larger and heavier flowers and fruits. The numbers of multi-petal flowers and multi-carpel fruits were greater in CsSUS4-OE plants compared with wild type and were regulated by MADS-box transcription factor. These results demonstrate that CsSUS4 plays important roles in the growth and development of cucumber flowers and fruits.

An Overview of Sucrose Synthases in Plants

Sucrose is the end product of photosynthesis and the primary sugar transported in the phloem of most plants. Sucrose synthase (SuSy) is a glycosyl transferase enzyme that plays a key role in sugar metabolism, primarily in sink tissues. SuSy catalyzes the reversible cleavage of sucrose into fructose and either uridine diphosphate glucose (UDP-G) or adenosine diphosphate glucose (ADP-G). The products of sucrose cleavage by SuSy are available for many metabolic pathways, such as energy production, primary-metabolite production, and the synthesis of complex carbohydrates. SuSy proteins are usually homotetramers with an average monomeric molecular weight of about 90 kD (about 800 amino acids long). Plant SuSy isozymes are mainly located in the cytosol or adjacent to plasma membrane, but some SuSy proteins are found in the cell wall, vacuoles, and mitochondria. Plant SUS gene families are usually small, containing between four to seven genes, with distinct exon-intron structures. Plant SUS genes are divided into three separate clades, which are present in both monocots and dicots. A comprehensive phylogenetic analysis indicates that a first SUS duplication event may have occurred before the divergence of the gymnosperms and angiosperms and a second duplication event probably occurred in a common angiosperm ancestor, leading to the existence of all three clades in both monocots and dicots. Plants with reduced SuSy activity have been shown to have reduced growth, reduced starch, cellulose or callose synthesis, reduced tolerance to anaerobic-stress conditions and altered shoot apical meristem function and leaf morphology. Plants overexpressing SUS have shown increased growth, increased xylem area and xylem cell-wall width, and increased cellulose and starch contents, making SUS high-potential candidate genes for the improvement of agricultural traits in crop plants. This review summarizes the current knowledge regarding plant SuSy, including newly discovered possible developmental roles for SuSy in meristem functioning that involve sugar and hormonal signaling.

Exploring natural genetic variation in tomato sucrose synthases on the basis of increased kinetic properties

Sucrose synthase (SuSy) is one key enzyme directly hydrolyzing sucrose to supply substrates for plant metabolism, and is considered to be a biomarker for plant sink strength. Improvement in plant sink strength could lead to enhanced plant growth and yield. Cultivated tomatoes are known to have a narrow genetic diversity, which hampers further breeding for novel and improved traits in new cultivars. In this study, we observed limited genetic variation in SuSy1, SuSy3 and SuSy4 in 53 accessions of cultivated tomato and landraces, but identified a wealth of genetic diversity in 32 accessions of related wild species. The variation in the deduced amino acid sequences was grouped into 23, 22, and 17 distinct haplotypes for SuSy1/3/4, respectively. Strikingly, all known substrate binding sites were highly conserved, as well as most of the phosphorylation sites except in SuSy1. Two SuSy1 and three SuSy3 protein variants were heterologously expressed to study the effect of the amino acid changes on enzyme kinetic properties, i.e. maximal sucrose hydrolyzing capacity (Vmax), affinity for sucrose (Km), and catalytic efficiency (Vmax/Km) at 25°C and 16°C. SuSy1-haplotype#3 containing phosphorylation site Ser-16 did not have an improvement in the kinetic properties compared to the reference SuSy1-haplotype#1 containing Arg-16. Meanwhile SuSy3-haplotype#9 from a wild accession, containing four amino acid changes S53A, S106I, E727D and K741E, showed an increase in Vmax/Km at 16°C compared to the reference SuSy3-haplotype#1. This study demonstrates that SuSy kinetic properties can be enhanced by exploiting natural variation, and the potential of this enzyme to improve sucrose metabolism and eventually sink strength in planta.

Thermo-responsive allele of sucrose synthase 3 (Sus3) provides high-temperature tolerance during the ripening stage in rice (Oryza sativa L.)

High-temperature stress during the ripening stage leads to quality deterioration due to an increase in chalky grains in brown rice (Oryza sativa L.). In a previous study, we identified a QTL for Appearance quality of brown rice 1 (Apq1) using chromosome segment substitution lines of the indica cultivar 'Habataki' in the japonica cultivar 'Koshihikari' background and narrowed down the locus to a 48-kb region on chromosome 7. To verify the function and mechanisms of this QTL in grain appearance, in this study, we fine-mapped the gene and conducted high-temperature tolerance tests. As a result of the genetic mapping, we narrowed down the candidate region of Apq1 to a 19.4-kb region including three predicted genes. Among these, the temporal expression pattern of sucrose synthase 3 (Sus3) corresponded well with the high temperature-sensitive period during ripening, and expression of the 'Habataki' allele of Sus3 was increased under high-temperature condition. In addition, we transformed the 'Habataki' Sus3 gene into 'Nipponbare', and the transformants obtained high-temperature tolerance. Therefore, we conclude that the causal gene underlying the QTL Apq1 is the thermo-responsive Sus3 allele, and the increase in Sus3 expression under high-temperature condition during ripening leads to high-temperature tolerance in rice.

Alternative routes for synthesis of N-linked glycans by Alg2 mannosyltransferase

Asparagine ( N)-linked glycosylation requires the ordered, stepwise synthesis of lipid-linked oligosaccharide (LLO) precursor Glc₃Man₉GlcNAc₂-pyrophosphate-dolichol (Glc₃Man₉Gn₂-PDol) on the endoplasmic reticulum. The fourth and fifth steps of LLO synthesis are catalyzed by Alg2, an unusual mannosyltransferase (MTase) with two different MTase activities; Alg2 adds both an α1,3- and α1,6-mannose onto ManGlcNAc₂-PDol to form the trimannosyl core Man₃GlcNAc₂-PDol. The biochemical properties of Alg2 are controversial and remain undefined. In this study, a liquid chromatography/mass spectrometry-based quantitative assay was established and used to analyze the MTase activities of purified yeast Alg2. Alg2-dependent Man₃GlcNAc₂-PDol production relied on net-neutral lipids with a propensity to form bilayers. We further showed addition of the α1,3- and α1,6-mannose can occur independently in either order but at differing rates. The conserved C-terminal EX₇E motif, N-terminal cytosolic tail, and 3 G-rich loop motifs in Alg2 play crucial roles for these activities, both in vitro and in vivo. These findings provide insight into the unique bifunctionality of Alg2 during LLO synthesis and lead to a new model in which alternative, independent routes exist for Alg2 catalysis of the trimannosyl core oligosaccharide.-Li, S.-T., Wang, N., Xu, X.-X., Fujita, M., Nakanishi, H., Kitajima, T., Dean, N., Gao, X.-D. Alternative routes for synthesis of N-linked glycans by Alg2 mannosyltransferase.